public class SmilesStereo
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
(package private) int |
atomCount |
(package private) int |
chiralClass |
(package private) int |
chiralOrder |
private java.lang.String |
details |
private java.lang.String |
directives |
private boolean |
isNot |
private Node[] |
jmolAtoms |
private int[][] |
polyhedralOrders |
private SmilesSearch |
search |
private PolyhedronStereoSorter |
sorter |
(package private) static int |
STEREOCHEMISTRY_ALLENE |
(package private) static int |
STEREOCHEMISTRY_DEFAULT |
(package private) static int |
STEREOCHEMISTRY_OCTAHEDRAL |
(package private) static int |
STEREOCHEMISTRY_POLYHEDRAL |
(package private) static int |
STEREOCHEMISTRY_SQUARE_PLANAR |
(package private) static int |
STEREOCHEMISTRY_TETRAHEDRAL |
(package private) static int |
STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL |
(package private) static int |
STEREOCHEMISTRY_TRIGONAL_PYRAMIDAL |
Constructor and Description |
---|
SmilesStereo(int chiralClass,
int chiralOrder,
int atomCount,
java.lang.String details,
java.lang.String directives) |
Modifier and Type | Method and Description |
---|---|
(package private) static int |
checkChirality(java.lang.String pattern,
int index,
SmilesAtom newAtom) |
boolean |
checkStereoChemistry(SmilesSearch smilesSearch,
VTemp v) |
(package private) static boolean |
checkStereochemistryAll(boolean isNot,
Node atom0,
int chiralClass,
int order,
Node atom1,
Node atom2,
Node atom3,
Node atom4,
Node atom5,
Node atom6,
VTemp v) |
(package private) static float |
distanceToPlane(javajs.util.V3 norm,
float w,
javajs.util.P3 pt) |
void |
fixStereo(SmilesAtom sAtom) |
int |
getChiralClass()
Returns the chiral class of the atom.
|
private static int |
getChiralityClass(java.lang.String xx) |
int |
getChiralOrder()
Returns the chiral order of the atom.
|
private static int |
getHandedness(Node a,
Node b,
Node c,
Node pt,
VTemp v)
compares the
|
private Node |
getJmolAtom(int i) |
private static void |
getPlaneNormals(Node atom1,
Node atom2,
Node atom3,
Node atom4,
VTemp v) |
private void |
getPolyhedralOrders() |
(package private) static java.lang.String |
getStereoFlag(Node atom0,
Node[] atoms,
int nAtoms,
VTemp v) |
private void |
getX(SmilesAtom sAtom,
Node[] jn,
int pt,
boolean haveCoordinates,
boolean needHSwitch) |
(package private) static boolean |
isDiaxial(Node atomA,
Node atomB,
Node atom1,
Node atom2,
VTemp v,
float f) |
static SmilesStereo |
newStereo(SmilesStereo stereo) |
void |
setChiralClass(int chiralClass)
Sets the chiral class of the atom.
|
void |
setChiralOrder(int chiralOrder)
Sets the chiral order of the atom.
|
private boolean |
setSmilesCoordinates(SmilesAtom atom,
SmilesAtom sAtom,
SmilesAtom sAtom2,
Node[] cAtoms) |
(package private) void |
sortBondsByStereo(Node atom,
Node atomPrev,
javajs.util.T3 ref,
Edge[] bonds,
javajs.util.V3 vTemp)
Sort bond array as ccw rotation around the axis connecting the atom and the
reference point (polyhedron center) as seen from outside the polyhedron
looking in.
|
int chiralClass
int chiralOrder
int atomCount
private java.lang.String details
private SmilesSearch search
private Node[] jmolAtoms
private java.lang.String directives
static final int STEREOCHEMISTRY_SQUARE_PLANAR
static final int STEREOCHEMISTRY_OCTAHEDRAL
static final int STEREOCHEMISTRY_TRIGONAL_BIPYRAMIDAL
static final int STEREOCHEMISTRY_TETRAHEDRAL
static final int STEREOCHEMISTRY_TRIGONAL_PYRAMIDAL
static final int STEREOCHEMISTRY_ALLENE
static final int STEREOCHEMISTRY_POLYHEDRAL
static final int STEREOCHEMISTRY_DEFAULT
private int[][] polyhedralOrders
private boolean isNot
private PolyhedronStereoSorter sorter
SmilesStereo(int chiralClass, int chiralOrder, int atomCount, java.lang.String details, java.lang.String directives) throws InvalidSmilesException
InvalidSmilesException
private static int getChiralityClass(java.lang.String xx)
public static SmilesStereo newStereo(SmilesStereo stereo) throws InvalidSmilesException
InvalidSmilesException
private void getPolyhedralOrders() throws InvalidSmilesException
InvalidSmilesException
public int getChiralClass()
CHIRALITY_...
constants)public void setChiralClass(int chiralClass)
CHIRALITY_...
constants)chiralClass
- Chiral class.public int getChiralOrder()
public void setChiralOrder(int chiralOrder)
chiralOrder
- Chiral order.public void fixStereo(SmilesAtom sAtom) throws InvalidSmilesException
InvalidSmilesException
private boolean setSmilesCoordinates(SmilesAtom atom, SmilesAtom sAtom, SmilesAtom sAtom2, Node[] cAtoms)
private void getX(SmilesAtom sAtom, Node[] jn, int pt, boolean haveCoordinates, boolean needHSwitch)
private Node getJmolAtom(int i)
void sortBondsByStereo(Node atom, Node atomPrev, javajs.util.T3 ref, Edge[] bonds, javajs.util.V3 vTemp)
atom
- atomPrev
- ref
- bonds
- vTemp
- public boolean checkStereoChemistry(SmilesSearch smilesSearch, VTemp v)
static java.lang.String getStereoFlag(Node atom0, Node[] atoms, int nAtoms, VTemp v)
atom0
- atoms
- nAtoms
- v
- static boolean checkStereochemistryAll(boolean isNot, Node atom0, int chiralClass, int order, Node atom1, Node atom2, Node atom3, Node atom4, Node atom5, Node atom6, VTemp v)
static boolean isDiaxial(Node atomA, Node atomB, Node atom1, Node atom2, VTemp v, float f)
private static int getHandedness(Node a, Node b, Node c, Node pt, VTemp v)
a
- b
- c
- pt
- v
- private static void getPlaneNormals(Node atom1, Node atom2, Node atom3, Node atom4, VTemp v)
static float distanceToPlane(javajs.util.V3 norm, float w, javajs.util.P3 pt)
static int checkChirality(java.lang.String pattern, int index, SmilesAtom newAtom) throws InvalidSmilesException
InvalidSmilesException